java获取sequence_Java Sequence.length方法代码示例

import org.biojava.bio.seq.Sequence; //导入方法依赖的package包/类

@Override

public Integer call() throws Exception {

PrintWriter writer = null;

try {

writer = writer(evalFile);

Sequence reference = readReference();

List scaffolds = readScaffolds();

writer.println("#reference length = " + reference.length());

writer.println("#scaffold count = " + scaffolds.size());

writer.println("#scaffold lengths = " + dumpLengths(scaffolds));

RangeSet ranges = TreeRangeSet.create();

for (HighScoringPair hsp : blastn(referenceFastaFile, scaffoldsFastaFile)) {

if (reference.getName().equals(hsp.target())) {

writer.println("#" + hsp.toString());

if (hsp.targetStart() <= hsp.targetEnd()) { // strands match

ranges.add(Range.closed(hsp.targetStart(), hsp.targetEnd()));

}

else {

ranges.add(Range.closed(hsp.targetEnd(), hsp.targetStart()));

}

}

}

writer.println("#coalesced intervals = " + ranges);

long breadthOfCoverage = 0;

for (Range range : ranges.asRanges()) {

breadthOfCoverage += ContiguousSet.create(range, DiscreteDomain.longs()).size();

}

double normalizedBreadthOfCoverage = (double) breadthOfCoverage / (double) reference.length();

writer.println("#breadth-of-coverage = " + breadthOfCoverage);

writer.println("#normalized breadth-of-coverage = " + normalizedBreadthOfCoverage);

StringBuilder sb = new StringBuilder();

sb.append(referenceFastaFile.getName());

sb.append("\t");

sb.append(scaffoldsFastaFile.getName());

sb.append("\t");

sb.append(reference.length());

sb.append("\t");

sb.append(scaffolds.size());

sb.append("\t");

sb.append(ranges.asRanges().size());

sb.append("\t");

sb.append(breadthOfCoverage);

sb.append("\t");

sb.append(normalizedBreadthOfCoverage);

sb.append("\t");

writer.println(sb.toString());

return 0;

}

finally {

try {

writer.close();

}

catch (Exception e) {

// ignore

}

}

}